Dear Prof. Case
Thank you for your useful information.
Kayo
2014-01-31 David A Case <case.biomaps.rutgers.edu>:
> On Fri, Jan 31, 2014, n.ricky0204.gmail.com wrote:
>>
>> I'm calculating the solvation free energy by rism3d.snglpnt in Ambertool 12.
>> I'd like to ask about the accuracy of the predicted solvation free
>> energy (rism_exchem).
>>
>> For example, the calculated solvation free energy of ethanol is +7.4
>> kcal/mol (closure=kh, water=tip3p), whereas the reported experimental
>> value is -5.01 kcal/mol.
>
> All hydration energies from 3D-RISM are too positive, but by a systematic
> amount. This appears to be related to the high internal pressure the theory
> predicts for water at its experimental density: it is too hard to make the
> cavity into which the solute molecule must fit.
>
>> And it has been shown that the uncorrected 3D-RISM approaches are not
>> able to provide quantitative description of hydration (J. Phys. Chem. B,
>> 2011, 115 (19), pp 6011-6022).
>
> There are lots of discussions of this point, and corrections are available,
> including in the paper you cited. See also:
>
> %A D.S. Palmer
> %A A.E. Frolov
> %A K.E. Ratkova
> %A M.V. Fedorov
> %T Towards a universal method for calculating hydration free energies: a 3D
> reference interaction site model with partial molar volume correction
> %J J. Phys. Condens. Matter
> %V 22
> %P 492101
> %D 2010
>
> [There is another paper by J.-F. Truchon et al. that should appear soon in
> JCTC addressing this issue.]
>
> The Amber output provides the computed partial molar volume, so you can apply
> the correction cited above yourself. I think(?) the next version of
> AmberTools will directly report some of these "corrected" values.
>
> Note that the electrostatic component of the hydration free energies appears
> to be rather good, so that there are many applications of RISM (aside from
> just looking at total hydration free energies) that do not require such
> corrections:
>
> %A T. Luchko
> %A I.S. Joung
> %A D.A. Case
> %T Integral equation theory of biomolecules and electrolytes
> %B Innovations in Biomolecular Modeling and Simulation, Volume 1
> %E T. Schlick
> %C London
> %I Royal Society of Chemistry
> %D 2012
> %P 51-86
>
> [There is another paper by J.-F. Truchon et al. that should appear soon in
> JCTC addressing this issue.]
>
> ...hope this helps....dac
>
>
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Received on Sat Feb 01 2014 - 04:00:02 PST
